How does pop protect you from storing email on a server you do not control? Only running your own mail server does that.
How does using pop protect you from the NSA? Only end to end encryption can attempt to do that.
Your argument makes no sense.
If I run my own server chances are it will be pop or imap. Idealy, the secure version which is encrypted. Though it's not so much about security, because you have no control over the path emails take going out or coming in, but it's about control. Doing your own backups, setting up the spam filtration that you want, etc. Also once email is on your server at least you know nobody can just go snoop at it any time. It's a bit more work to go look at packet logs and I would imagine those get purged after a while as the internet as a whole produces TONS of packet data so the NSA can only store so much of it. Maybe a years worth or so, if that.